We have investigated the regulation of neuronal calcium by using electron energy-loss spectroscopic (EELS) imaging to map elemental distributions in frog sympathetic ganglia at high spatial resolution in the scanning transmission electron microscope (STEM). The neurons, which were prepared by rapid freezing and cryosectioning, accumulated calcium within their mitochondria in the period of a few minutes after depolarization. Elemental maps, obtained by subtracting the EELS spectral background at each pixel, revealed a radial dependence of this calcium concentration within the cell: peripheral mitochondria accumulated abundant small ten-nanometer sized calcium and phosphorus-rich deposits within their matrix, whereas centrally located mitochondria contained few such deposits. Quantitative analysis of the mitochondrial matrix showed low millimole/kg calcium concentrations. Furthermore, the small mineral-like inclusions disappeared in neurons that were allowed to recover from the effects of depolarization. To measure the much lower levels of calcium in the endoplasmic reticulum it was necessary to sum over many pixels in the spectrum-images. Radial distributions of ER calcium exhibited an inverse relationship with mitochondrial calcium. The results of these experiments indicated that mitochondria retain a record of early spatial differences in intracellular calcium long after such gradients have dissipated.